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Conserved domains on  [gi|30474871|ref|NP_847894|]
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serine palmitoyltransferase 1 isoform b [Homo sapiens]

Protein Classification

PLP-dependent aminotransferase family protein( domain architecture ID 139552)

PLP-dependent aminotransferase family protein may combine pyridoxal phosphate with an alpha-amino acid to form a Schiff base or aldimine intermediate, which then acts as the substrate in a reaction such as a transamination, racemization, or decarboxylation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AAT_I super family cl18945
Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP) ...
 11-141 8.60e-35

Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V).


The actual alignment was detected with superfamily member PLN02822:

Pssm-ID: 450240 [Multi-domain]  Cd Length: 481  Bit Score: 125.62  E-value: 8.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30474871   11 VEMVQALYEAPAY-----------HLILEGILILWIIRLLFSKTYKLQERSdLTVKEKEELIEEWQPEPLVPPVPK---- 75
Cdd:PLN02822  13 LERVTMLLEAPLAravvfgvhiggHLVVEGLLIVVIVFLLSQKSYKPPKRP-LTEKEIDELCDEWTPEPLIPPITEemrp 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30474871   76 DHPALNYniVSGPpshKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGT 141
Cdd:PLN02822  92 EPPVLES--AAGP---HTIINGKDVVNFASANYLGLIGNEKIKESCTSALEKYGVGSCGPRGFYGT 152
 
Name Accession Description Interval E-value
PLN02822 PLN02822
serine palmitoyltransferase
 11-141 8.60e-35

serine palmitoyltransferase


Pssm-ID: 178417 [Multi-domain]  Cd Length: 481  Bit Score: 125.62  E-value: 8.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30474871   11 VEMVQALYEAPAY-----------HLILEGILILWIIRLLFSKTYKLQERSdLTVKEKEELIEEWQPEPLVPPVPK---- 75
Cdd:PLN02822  13 LERVTMLLEAPLAravvfgvhiggHLVVEGLLIVVIVFLLSQKSYKPPKRP-LTEKEIDELCDEWTPEPLIPPITEemrp 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30474871   76 DHPALNYniVSGPpshKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGT 141
Cdd:PLN02822  92 EPPVLES--AAGP---HTIINGKDVVNFASANYLGLIGNEKIKESCTSALEKYGVGSCGPRGFYGT 152
BioF COG0156
7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]; ...
 84-143 4.25e-12

7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]; 7-keto-8-aminopelargonate synthetase or related enzyme is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 439926 [Multi-domain]  Cd Length: 385  Bit Score: 61.99  E-value: 4.25e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30474871  84 IVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE 143
Cdd:COG0156  23 VLESPQGPRVTIDGREVLNFSSNDYLGLANHPRVIEAAAEALDRYGTGSGGSRLVSGTTP 82
KBL_like cd06454
KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate ...
 98-143 1.78e-10

KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.


Pssm-ID: 99747 [Multi-domain]  Cd Length: 349  Bit Score: 57.19  E-value: 1.78e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30474871  98 KECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE 143
Cdd:cd06454   1 KKVLNFCSNDYLGLANHPEVIEAAKEALDKYGVGAGGSRLISGTSD 46
 
Name Accession Description Interval E-value
PLN02822 PLN02822
serine palmitoyltransferase
 11-141 8.60e-35

serine palmitoyltransferase


Pssm-ID: 178417 [Multi-domain]  Cd Length: 481  Bit Score: 125.62  E-value: 8.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30474871   11 VEMVQALYEAPAY-----------HLILEGILILWIIRLLFSKTYKLQERSdLTVKEKEELIEEWQPEPLVPPVPK---- 75
Cdd:PLN02822  13 LERVTMLLEAPLAravvfgvhiggHLVVEGLLIVVIVFLLSQKSYKPPKRP-LTEKEIDELCDEWTPEPLIPPITEemrp 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30474871   76 DHPALNYniVSGPpshKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGT 141
Cdd:PLN02822  92 EPPVLES--AAGP---HTIINGKDVVNFASANYLGLIGNEKIKESCTSALEKYGVGSCGPRGFYGT 152
PLN03227 PLN03227
serine palmitoyltransferase-like protein; Provisional
 101-143 2.89e-12

serine palmitoyltransferase-like protein; Provisional


Pssm-ID: 178766 [Multi-domain]  Cd Length: 392  Bit Score: 62.61  E-value: 2.89e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 30474871  101 INFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE 143
Cdd:PLN03227   1 LNFATHDFLSTSSSPTLRQTALESLSHYGCGSCGPRGFYGTID 43
BioF COG0156
7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]; ...
 84-143 4.25e-12

7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]; 7-keto-8-aminopelargonate synthetase or related enzyme is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 439926 [Multi-domain]  Cd Length: 385  Bit Score: 61.99  E-value: 4.25e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30474871  84 IVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE 143
Cdd:COG0156  23 VLESPQGPRVTIDGREVLNFSSNDYLGLANHPRVIEAAAEALDRYGTGSGGSRLVSGTTP 82
KBL_like cd06454
KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate ...
 98-143 1.78e-10

KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.


Pssm-ID: 99747 [Multi-domain]  Cd Length: 349  Bit Score: 57.19  E-value: 1.78e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30474871  98 KECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE 143
Cdd:cd06454   1 KKVLNFCSNDYLGLANHPEVIEAAKEALDKYGVGAGGSRLISGTSD 46
PRK06939 PRK06939
2-amino-3-ketobutyrate coenzyme A ligase; Provisional
 84-143 3.61e-10

2-amino-3-ketobutyrate coenzyme A ligase; Provisional


Pssm-ID: 235893 [Multi-domain]  Cd Length: 397  Bit Score: 56.36  E-value: 3.61e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30474871   84 IVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFE 143
Cdd:PRK06939  28 ITSPQGADITVADGKEVINFCANNYLGLANHPELIAAAKAALDSHGFGMASVRFICGTQD 87
PRK05958 PRK05958
8-amino-7-oxononanoate synthase; Reviewed
 84-136 3.83e-08

8-amino-7-oxononanoate synthase; Reviewed


Pssm-ID: 235655 [Multi-domain]  Cd Length: 385  Bit Score: 50.54  E-value: 3.83e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 30474871   84 IVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPR 136
Cdd:PRK05958  25 PREGGAGRWLVVDGRRMLNFASNDYLGLARHPRLIAAAQQAARRYGAGSGGSR 77
PLN02483 PLN02483
serine palmitoyltransferase
 96-141 9.23e-06

serine palmitoyltransferase


Pssm-ID: 178101 [Multi-domain]  Cd Length: 489  Bit Score: 43.98  E-value: 9.23e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 30474871   96 NGKECINFASFNFLGLLD-----NPRVkaaaLASLKKYGVGTCGPRGFYGT 141
Cdd:PLN02483  98 KTRRCLNLGSYNYLGFAAadeycTPRV----IESLKKYSASTCSSRVDGGT 144
PRK07505 PRK07505
hypothetical protein; Provisional
 83-130 3.02e-03

hypothetical protein; Provisional


Pssm-ID: 181006 [Multi-domain]  Cd Length: 402  Bit Score: 36.50  E-value: 3.02e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 30474871   83 NIVSGPPSHK--TVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGV 130
Cdd:PRK07505  29 GLTVGEREGIliTLADGHTFVNFVSCSYLGLDTHPAIIEGAVDALKRTGS 78
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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